# Bio.Align.tabular module

Bio.Align support for tabular output from BLAST or FASTA.

This module contains a parser for tabular output from BLAST run with the ‘-outfmt 7’ argument, as well as tabular output from William Pearson’s FASTA alignment tools using the ‘-m 8CB’ or ‘-m 8CC’ arguments.

class Bio.Align.tabular.State(value, names=_not_given, *values, module=None, qualname=None, type=None, start=1, boundary=None)

  Bases: `Enum`

  Enumerate alignment states needed when parsing a BTOP string.

  MATCH = 1
  QUERY_GAP = 2
  TARGET_GAP = 3
  NONE = 4

class Bio.Align.tabular.AlignmentIterator(source)

  Bases: `AlignmentIterator`

  Alignment iterator for tabular output from BLAST or FASTA.

  For reading (pairwise) alignments from tabular output generated by BLAST run with the ‘-outfmt 7’ argument, as well as tabular output generated by William Pearson’s FASTA alignment programs with the ‘-m 8CB’ or ‘-m 8CC’ output formats.

  fmt: str | None = 'Tabular'
  parse_btop(btop)

    Parse a BTOP string and return alignment coordinates.

    A BTOP (Blast trace-back operations) string is used by BLAST to describe a sequence alignment.

  parse_cigar(cigar)

    Parse a CIGAR string and return alignment coordinates.

    A CIGAR string, as defined by the SAM Sequence Alignment/Map format, describes a sequence alignment as a series of lengths and operation (alignment/insertion/deletion) codes.

  __abstractmethods__ = frozenset({})
  __annotations__ = {'fmt': 'Optional[str]'}
  __firstlineno__ = 34
  __static_attributes__ = ('_fields', '_final_prefix', '_query_description', '_query_id', '_query_size', 'metadata')

Biopython v: 1.85

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